It's a deep subject, like how you can have KR without misfires. Misfires w/o KR etc. I reread a little here and you said you dropped 3 cylinders. Take a look at your torque management and fuel injector rpm etc limiting tables. Your pcm will disable 3 injectors for certain reasons when it feels limits or abuse is occuring etc. It'll also screw with AFR etc... this is all if you haven't had this stuff adjusted from factory though.